vbim(1) [debian man page]

vbim(1) 							 The VoxBo Manual							   vbim(1)

NAME

       vbim - manipulate 3D and 4D volumes

SYNOPSIS

       vbim <flag> ...

DESCRIPTION

       vbim is part of the VoxBo suite of tools for brain image analysis.

       vbim is a multi-purpose program that applies various simple manipulations to 3D and 4D images.

OPTIONS

       vbim performs a set of operations, specified by option flags, in sequence.  To get a complete list of available flags, run the program with
       no arguments.

EXAMPLES

       To get very basic info about a file:

	      vbim foo.nii -info

       To get more detailed information about the data within a mask:

	      vbim foo.nii -regioninfo mask.nii

       To apply a mask to a 3D image and write out the result:

	      vbim image.nii -mask mask.nii -write maskedimage.nii

       To mask a 4D image:

	      vbim image.nii -mask mask.nii -write4D maskedimage.nii

       To average a bunch of 3D volumes:

	      vbim *.nii.gz -average -write mean.nii.gz

       To create a lesion count map from a set of lesion masks:

	      vbim *.nii -count -write count.nii.gz

       To create a 4D volume (20x20x20 voxels, 32-bit int, 10 time points) of random data with a mean of 100 and sd of 10:

	      vbim -newvol 20 20 20 10 int32 -addnoise 100 10 -write3d myvol.nii

NOTES

AVAILABILITY

       Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and via the NeuroDebian project (neuro.debian.net)  for  Debian  deriva-
       tives.

CAVEATS

       VoxBo is provided with no warranty whatsoever.

AUTHOR

       For an historical roster of the VoxBo development team, visit www.voxbo.org.

SEE ALSO

       For  detailed  help  on	any VoxBo command-line program, run it with no arguments.  For graphical programs, use the -h flag.  For more help
       with VoxBo, for information about the mailing list, or to report bugs, visit the web site at www.voxbo.org.

       For information about file format support in VoxBo, see voxbo-fileformats(7).  For general information about VoxBo, see voxbo(7).

VoxBo							      January, 2011 (v1.8.5)							   vbim(1)

voxbo-fileformats(7)						 The VoxBo Manual					      voxbo-fileformats(7)

NAME

       voxbo-fileformats - general information about file format support in VoxBo

DESCRIPTION

       The  VoxBo  suite  of tools for brain image analysis supports a variety of formats for 1D (vector), 2D (matrix), 3D (volume) and 4D (volume
       time series) data.

       File format support in VoxBo is modular - most of the tools can read and write any supported file format transparently,	with  output  file
       formats usually determined by the file extension.

       The  i/o  library  supports several special access methods.  For 4D files, filename:mask is used to access the inclusion mask of a 4D file.
       The mask is treated as a 3D volume.  Similarly, filename:n accesses the nth volume of the 4D series in filename, where n is an integer  and
       the first volume is numbered 0.

       When writing, VoxBo honors filename tags that can be used to specify the fileformat or byteorder.  Tags are specified in square brackets at
       the end of the filename, and multiple tags can be separated within the brackets by commas.  For example, foo[imgdir] can be used to specify
       the  imgdir file format (useful because imgdir format doesn't have a standard extension).  foo.nii[little] forces little-endian storage for
       file formats that allow it.

   VoxBo native file formats
       VoxBo's native file formats, all supported for read and write, include .ref (1D), .mat (2D), .cub (3D), and .tes (4D).  Although these for-
       mats are not widely supported in external software, they offer some useful features, including user-editable text headers.  gzip-compressed
       cub and tes files are supported transparently.

   NIfTI
       VoxBo supports 3D and 4D NIfTI files (compressed or not) for read and write.   VoxBo  does  not	currently  make  intelligent  use  of  the
       qform/sform orientation information.

   Analyze
       VoxBo  supports	SPM-style  Analyze(TM)	files,	including 3D and 4D files, as well as 4D time series composed of directories containing 3D
       files, for read/write.  All individual files are stored in .img/.hdr pairs.

   DICOM
       VoxBo supports DICOM (as well as some DICOM-like files in the older ACR/NEMA format) for reading only.  VoxBo  supports	a  corner  of  the
       DICOM  standard	frequently encountered in brain imaging research, including mosaic format volumes.  Files containing single slice data are
       read as 3D volumes.  Directories containing multiple files are generally parsed as 3D or 4D data, as appropriate, as long as no	extraneous
       files are in the directory.

   Text Matrices and Vectors
       Plain text files containing just numbers (or comment lines beginning with #, %, or ;), can be parsed as matrix or vector data.

EXAMPLES

AVAILABILITY

       Pre-built  VoxBo  binaries  are available for Linux, OSX, and Cygwin, and via the NeuroDebian project (neuro.debian.net) for Debian deriva-
       tives.

CAVEATS

       VoxBo is provided with no warranty whatsoever.

AUTHOR

       For an historical roster of the VoxBo development team, visit www.voxbo.org.

SEE ALSO

       For detailed help on any VoxBo command-line program, run it with no arguments.  For graphical programs, use the -h  flag.   For	more  help
       with VoxBo, for information about the mailing list, or to report bugs, visit the web site at www.voxbo.org.

       For general information about VoxBo, see voxbo(7).

VoxBo							      January, 2011 (v1.8.5)					      voxbo-fileformats(7)